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Split away CTMatrix, TMatrixInterpolator 

Former-commit-id: ca92a0938f12fda858794b203e196366f2466a6f
This commit is contained in:
Marek Nečada 2019-08-10 09:55:50 +03:00
parent 6ea386d759
commit 1aa64248fc
6 changed files with 157 additions and 130 deletions
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1
qpms/__init__.py
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@ -5,6 +5,7 @@ from .qpms_c import *
from .qpms_p import *
from .cyquaternions import CQuat, IRot3
from .cybspec import VSWFNorm, BaseSpec
from .cytmatrices import CTMatrix, TMatrixInterpolator
from .cytranslations import trans_calculator
from .cymaterials import MaterialInterpolator
from .lattices2d import *

25
qpms/cytmatrices.pxd Normal file
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@ -0,0 +1,25 @@
cimport numpy as np
from qpms_cdefs cimport qpms_tmatrix_t, cdouble, qpms_tmatrix_interpolator_t
from cybspec cimport BaseSpec
cdef class TMatrixInterpolator:
#cdef readonly np.ndarray m # Numpy array holding the matrix data
cdef readonly BaseSpec spec # Here we hold the base spec for the correct reference counting; TODO check if it gets copied
cdef qpms_tmatrix_t *tmatrices_array
cdef cdouble *tmdata
cdef double *freqs
cdef double *freqs_su
cdef size_t nfreqs
cdef qpms_tmatrix_interpolator_t *interp
cdef class CTMatrix: # N.B. there is another type called TMatrix in tmatrices.py!
cdef readonly np.ndarray m # Numpy array holding the matrix data
cdef readonly BaseSpec spec # Here we hold the base spec for the correct reference counting; TODO check if it gets copied
cdef qpms_tmatrix_t t
cdef inline qpms_tmatrix_t *rawpointer(CTMatrix self):
'''Pointer to the qpms_tmatrix_t structure.
Don't forget to reference the BaseSpec object itself when storing the pointer anywhere!!!
'''
return &(self.t)

116
qpms/cytmatrices.pyx Normal file
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@ -0,0 +1,116 @@
import numpy as np
from qpms_cdefs cimport *
from cybspec cimport BaseSpec
from cycommon import *
from cycommon cimport make_c_string
from qpms_c cimport FinitePointGroup
import warnings
import os
from libc.stdlib cimport free
cdef class TMatrixInterpolator:
'''
Wrapper over the qpms_tmatrix_interpolator_t structure.
'''
def __cinit__(self, filename, BaseSpec bspec, *args, **kwargs):
'''Creates a T-matrix interpolator object from a scuff-tmatrix output'''
global qpms_load_scuff_tmatrix_crash_on_failure
qpms_load_scuff_tmatrix_crash_on_failure = False
self.spec = bspec
cdef char * cpath = make_c_string(filename)
retval = qpms_load_scuff_tmatrix(cpath, self.spec.rawpointer(),
&(self.nfreqs), &(self.freqs), &(self.freqs_su),
&(self.tmatrices_array), &(self.tmdata))
if (retval != QPMS_SUCCESS):
raise IOError("Could not read T-matrix from %s: %s" % (filename, os.strerror(retval)))
if 'symmetrise' in kwargs:
sym = kwargs['symmetrise']
if isinstance(sym, FinitePointGroup):
if QPMS_SUCCESS != qpms_symmetrise_tmdata_finite_group(
self.tmdata, self.nfreqs, self.spec.rawpointer(),
(<FinitePointGroup?>sym).rawpointer()):
raise Exception("This should not happen.")
atol = kwargs['atol'] if 'atol' in kwargs else 1e-16
qpms_czero_roundoff_clean(self.tmdata, self.nfreqs * len(bspec)**2, atol)
else:
warnings.warn('symmetrise argument type not supported; ignoring.')
self.interp = qpms_tmatrix_interpolator_create(self.nfreqs,
self.freqs, self.tmatrices_array, gsl_interp_cspline)
if not self.interp: raise Exception("Unexpected NULL at interpolator creation.")
def __call__(self, double freq):
'''Returns a TMatrix instance, corresponding to a given frequency.'''
if freq < self.freqs[0] or freq > self.freqs[self.nfreqs-1]:# FIXME here I assume that the input is already sorted
raise ValueError("input frequency %g is outside the interpolator domain (%g, %g)"
% (freq, self.freqs[0], self.freqs[self.nfreqs-1]))
# This is a bit stupid, I should rethink the CTMatrix constuctors
cdef qpms_tmatrix_t *t = qpms_tmatrix_interpolator_eval(self.interp, freq)
cdef CTMatrix res = CTMatrix(self.spec, <cdouble[:len(self.spec),:len(self.spec)]>(t[0].m))
qpms_tmatrix_free(t)
return res
def __dealloc__(self):
qpms_tmatrix_interpolator_free(self.interp)
free(self.tmatrices_array)
free(self.tmdata)
free(self.freqs_su)
free(self.freqs)
property freq_interval:
def __get__(self):
return [self.freqs[0], self.freqs[self.nfreqs-1]]
cdef class CTMatrix: # N.B. there is another type called TMatrix in tmatrices.py!
'''
Wrapper over the C qpms_tmatrix_t stucture.
'''
def __cinit__(CTMatrix self, BaseSpec spec, matrix):
self.spec = spec
self.t.spec = self.spec.rawpointer();
if (matrix is None) or not np.any(matrix):
self.m = np.zeros((len(spec),len(spec)), dtype=complex, order='C')
else:
# The following will raise an exception if shape is wrong
self.m = np.array(matrix, dtype=complex, copy=True, order='C').reshape((len(spec), len(spec)))
#self.m.setflags(write=False) # checkme
cdef cdouble[:,:] m_memview = self.m
self.t.m = &(m_memview[0,0])
self.t.owns_m = False # Memory in self.t.m is "owned" by self.m, not by self.t...
property rawpointer:
def __get__(self):
return <uintptr_t> &(self.t)
# Transparent access to the T-matrix elements.
def __getitem__(self, key):
return self.m[key]
def __setitem__(self, key, value):
self.m[key] = value
def as_ndarray(CTMatrix self):
''' Returns a copy of the T-matrix as a numpy array.'''
# Maybe not totally needed after all, as np.array(T[...]) should be equivalent and not longer
return np.array(self.m, copy=True)
def spherical_fill(CTMatrix self, double radius, cdouble k_int,
cdouble k_ext, cdouble mu_int = 1, cdouble mu_ext = 1):
''' Replaces the contents of the T-matrix with those of a spherical particle.'''
qpms_tmatrix_spherical_fill(&self.t, radius, k_int, k_ext, mu_int, mu_ext)
def spherical_perm_fill(CTMatrix self, double radius, double freq, cdouble epsilon_int,
cdouble epsilon_ext):
'''Replaces the contenst of the T-matrix with those of a spherical particle.'''
qpms_tmatrix_spherical_mu0_fill(&self.t, radius, freq, epsilon_int, epsilon_ext)
@staticmethod
def spherical(BaseSpec spec, double radius, cdouble k_int, cdouble k_ext,
cdouble mu_int = 1, cdouble mu_ext = 1):
''' Creates a T-matrix of a spherical nanoparticle. '''
tm = CTMatrix(spec, 0)
tm.spherical_fill(radius, k_int, k_ext, mu_int, mu_ext)
return tm
@staticmethod
def spherical_perm(BaseSpec spec, double radius, double freq, cdouble epsilon_int, cdouble epsilon_ext):
'''Creates a T-matrix of a spherical nanoparticle.'''
tm = CTMatrix(spec, 0)
tm.spherical_perm_fill(radius, freq, epsilon_int, epsilon_ext)
return tm

8
qpms/qpms_c.pxd Normal file
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@ -0,0 +1,8 @@
from qpms_cdefs cimport qpms_finite_group_t
cdef class FinitePointGroup:
cdef readonly bint owns_data
cdef qpms_finite_group_t *G
cdef inline qpms_finite_group_t *rawpointer(self):
return self.G

130
qpms/qpms_c.pyx
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@ -16,136 +16,13 @@ from cybspec cimport *
#from cybspec import *
from cycommon import *
from cycommon cimport make_c_string
from cytmatrices cimport CTMatrix
cimport cython
import enum
import warnings
import os
from libc.stdlib cimport malloc, free, calloc, abort
cdef class TMatrixInterpolator:
'''
Wrapper over the qpms_tmatrix_interpolator_t structure.
'''
#cdef readonly np.ndarray m # Numpy array holding the matrix data
cdef readonly BaseSpec spec # Here we hold the base spec for the correct reference counting; TODO check if it gets copied
cdef qpms_tmatrix_t *tmatrices_array
cdef cdouble *tmdata
cdef double *freqs
cdef double *freqs_su
cdef size_t nfreqs
cdef qpms_tmatrix_interpolator_t *interp
def __cinit__(self, filename, BaseSpec bspec, *args, **kwargs):
'''Creates a T-matrix interpolator object from a scuff-tmatrix output'''
global qpms_load_scuff_tmatrix_crash_on_failure
qpms_load_scuff_tmatrix_crash_on_failure = False
self.spec = bspec
cdef char * cpath = make_c_string(filename)
retval = qpms_load_scuff_tmatrix(cpath, self.spec.rawpointer(),
&(self.nfreqs), &(self.freqs), &(self.freqs_su),
&(self.tmatrices_array), &(self.tmdata))
if (retval != QPMS_SUCCESS):
raise IOError("Could not read T-matrix from %s: %s" % (filename, os.strerror(retval)))
if 'symmetrise' in kwargs:
sym = kwargs['symmetrise']
if isinstance(sym, FinitePointGroup):
if QPMS_SUCCESS != qpms_symmetrise_tmdata_finite_group(
self.tmdata, self.nfreqs, self.spec.rawpointer(),
(<FinitePointGroup?>sym).rawpointer()):
raise Exception("This should not happen.")
atol = kwargs['atol'] if 'atol' in kwargs else 1e-16
qpms_czero_roundoff_clean(self.tmdata, self.nfreqs * len(bspec)**2, atol)
else:
warnings.warn('symmetrise argument type not supported; ignoring.')
self.interp = qpms_tmatrix_interpolator_create(self.nfreqs,
self.freqs, self.tmatrices_array, gsl_interp_cspline)
if not self.interp: raise Exception("Unexpected NULL at interpolator creation.")
def __call__(self, double freq):
'''Returns a TMatrix instance, corresponding to a given frequency.'''
if freq < self.freqs[0] or freq > self.freqs[self.nfreqs-1]:# FIXME here I assume that the input is already sorted
raise ValueError("input frequency %g is outside the interpolator domain (%g, %g)"
% (freq, self.freqs[0], self.freqs[self.nfreqs-1]))
# This is a bit stupid, I should rethink the CTMatrix constuctors
cdef qpms_tmatrix_t *t = qpms_tmatrix_interpolator_eval(self.interp, freq)
cdef CTMatrix res = CTMatrix(self.spec, <cdouble[:len(self.spec),:len(self.spec)]>(t[0].m))
qpms_tmatrix_free(t)
return res
def __dealloc__(self):
qpms_tmatrix_interpolator_free(self.interp)
free(self.tmatrices_array)
free(self.tmdata)
free(self.freqs_su)
free(self.freqs)
property freq_interval:
def __get__(self):
return [self.freqs[0], self.freqs[self.nfreqs-1]]
cdef class CTMatrix: # N.B. there is another type called TMatrix in tmatrices.py!
'''
Wrapper over the C qpms_tmatrix_t stucture.
'''
cdef readonly np.ndarray m # Numpy array holding the matrix data
cdef readonly BaseSpec spec # Here we hold the base spec for the correct reference counting; TODO check if it gets copied
cdef qpms_tmatrix_t t
def __cinit__(CTMatrix self, BaseSpec spec, matrix):
self.spec = spec
self.t.spec = self.spec.rawpointer();
if (matrix is None) or not np.any(matrix):
self.m = np.zeros((len(spec),len(spec)), dtype=complex, order='C')
else:
# The following will raise an exception if shape is wrong
self.m = np.array(matrix, dtype=complex, copy=True, order='C').reshape((len(spec), len(spec)))
#self.m.setflags(write=False) # checkme
cdef cdouble[:,:] m_memview = self.m
self.t.m = &(m_memview[0,0])
self.t.owns_m = False # Memory in self.t.m is "owned" by self.m, not by self.t...
cdef qpms_tmatrix_t *rawpointer(CTMatrix self):
'''Pointer to the qpms_tmatrix_t structure.
Don't forget to reference the BaseSpec object itself when storing the pointer anywhere!!!
'''
return &(self.t)
property rawpointer:
def __get__(self):
return <uintptr_t> &(self.t)
# Transparent access to the T-matrix elements.
def __getitem__(self, key):
return self.m[key]
def __setitem__(self, key, value):
self.m[key] = value
def as_ndarray(CTMatrix self):
''' Returns a copy of the T-matrix as a numpy array.'''
# Maybe not totally needed after all, as np.array(T[...]) should be equivalent and not longer
return np.array(self.m, copy=True)
def spherical_fill(CTMatrix self, double radius, cdouble k_int,
cdouble k_ext, cdouble mu_int = 1, cdouble mu_ext = 1):
''' Replaces the contents of the T-matrix with those of a spherical particle.'''
qpms_tmatrix_spherical_fill(&self.t, radius, k_int, k_ext, mu_int, mu_ext)
def spherical_perm_fill(CTMatrix self, double radius, double freq, cdouble epsilon_int,
cdouble epsilon_ext):
'''Replaces the contenst of the T-matrix with those of a spherical particle.'''
qpms_tmatrix_spherical_mu0_fill(&self.t, radius, freq, epsilon_int, epsilon_ext)
@staticmethod
def spherical(BaseSpec spec, double radius, cdouble k_int, cdouble k_ext,
cdouble mu_int = 1, cdouble mu_ext = 1):
''' Creates a T-matrix of a spherical nanoparticle. '''
tm = CTMatrix(spec, 0)
tm.spherical_fill(radius, k_int, k_ext, mu_int, mu_ext)
return tm
@staticmethod
def spherical_perm(BaseSpec spec, double radius, double freq, cdouble epsilon_int, cdouble epsilon_ext):
'''Creates a T-matrix of a spherical nanoparticle.'''
tm = CTMatrix(spec, 0)
tm.spherical_perm_fill(radius, freq, epsilon_int, epsilon_ext)
return tm
cdef class PointGroup:
cdef readonly qpms_pointgroup_t G
@ -196,8 +73,6 @@ cdef class FinitePointGroup:
TODO more functionality to make it better usable in Python
(group element class at least)
'''
cdef readonly bint owns_data
cdef qpms_finite_group_t *G
def __cinit__(self, info):
'''Constructs a FinitePointGroup from PointGroupInfo'''
@ -284,9 +159,6 @@ cdef class FinitePointGroup:
self.G = <qpms_finite_group_t *>0
self.owns_data = False
cdef qpms_finite_group_t *rawpointer(self):
return self.G
cdef class FinitePointGroupElement:
'''TODO'''
cdef readonly FinitePointGroup G

7
setup.py
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@ -87,6 +87,11 @@ cycommon = Extension('qpms.cycommon',
extra_link_args=['qpms/libqpms.a'],
libraries=['gsl', 'lapacke', 'blas', 'gslcblas', 'pthread',]
)
cytmatrices = Extension('qpms.cytmatrices',
sources = ['qpms/cytmatrices.pyx'],
extra_link_args=['qpms/libqpms.a', 'amos/libamos.a'],
libraries=['gsl', 'lapacke', 'blas', 'gslcblas', 'pthread',]
)
cytranslations = Extension('qpms.cytranslations',
sources = ['qpms/cytranslations.pyx',
'qpms/translations_python.c',
@ -135,7 +140,7 @@ setup(name='qpms',
#'quaternion','spherical_functions',
'scipy>=0.18.0', 'sympy>=1.2'],
#dependency_links=['https://github.com/moble/quaternion/archive/v2.0.tar.gz','https://github.com/moble/spherical_functions/archive/master.zip'],
ext_modules=cythonize([qpms_c, cytranslations, cycommon, cyquaternions, cybspec, cymaterials], include_path=['qpms', 'amos'], gdb_debug=True),
ext_modules=cythonize([qpms_c, cytranslations, cytmatrices, cycommon, cyquaternions, cybspec, cymaterials], include_path=['qpms', 'amos'], gdb_debug=True),
cmdclass = {'build_ext': build_ext},
zip_safe=False
)